Mitochondrial DNA reveals the natal origin of Caretta caretta (Testudines: Cheloniidae) stranded or bycaught along the Southwestern Adriatic coasts

References

• Abreu-Grobois FA , Horrocks J , Formia A , Dutton PH , LeRoux R , Vélez-Zuazo X , Soares L , Meylan P 2006. New mtDNA Dloop primers which work for a variety of marine turtle species may increase the resolution of mixed stock analyses. Proceedings of the 26th Annual Symposium on Sea Turtle Biology Conservation, 3–8 April 2006, Crete. p. 179.
   Google Scholar
• Benbouza H , Jacquemin JM , Baudoin JP , Mergeai G. 2006. Optimization of reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnology, Agronomy, Society and Environment 10:77–81.
   Google Scholar
• Bentivegna F. 2002. Intra-Mediterranean migrations of loggerhead sea turtles (Caretta caretta) monitored by satellite telemetry. Marine Biology 141:795–800. DOI: 10.1007/s00227-002-0856-z.
   Web of Science ®Google Scholar
• Bolker B 2012. mixstock: functions for mixed stock analysis. R package version 0.9.5.1. Available: http://cran.r-project.org/web/packages/mixstock/index.html . Accessed Oct 2017 30.
   Google Scholar
• Bolten AB . 1999. Techniques for measuring sea turtles. In: Eckert KL , Bjorndal KA , Abreu-Grobois FA , Donnelly M , editors. Research and management techniques for the conservation of sea turtles. Washington: IUCN/SSC Marine Turtle Specialist Group. pp. 110–114.
   Google Scholar
• Bolten AB . 2003. Variation in sea turtle life history patterns: Neritic versus oceanic developmental stages. In: Lutz PL , Musick JA , Wyneken J , editors. The biology of sea turtles. Boca Raton: CRC Press. pp. 243–257.
   Google Scholar
• Bowen BW , Kamezaki N , Limpus CJ , Hughes GR , Meylan AB , Avise JC . 1994. Global phylogeography of the loggerhead turtle (Caretta caretta) as indicated by mitochondrial DNA haplotypes. Evolution 48:1820–1828.
   Web of Science ®Google Scholar
• Broderick AC , Glen F , Godley BJ , Hays GC . 2002. Estimating the number of green and loggerhead turtles nesting annually in the Mediterranean. Oryx 36:227–235. DOI: 10.1017/S0030605302000431.
   Web of Science ®Google Scholar
• Carreras C , Pascual M , Cardona L , Aguilar A , Margaritoulis D , Rees A , Turkozan O , Levy Y , Gasith A , Aureggi M , Khalil M . 2007. The genetic structure of the loggerhead sea turtle (Caretta caretta) in the Mediterranean as revealed by nuclear and mitochondrial DNA and its conservation implications. Conservation Genetics 8:761–775. DOI: 10.1007/s10592-006-9224-8.
   Web of Science ®Google Scholar
• Carreras C , Pont S , Maffucci F , Pascual M , Barceló A , Bentivegna F , Cardona L , Alegre F , SanFélix M , Fernández G , Aguilar A . 2006. Genetic structuring of immature loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea reflects water circulation patterns. Marine Biology 149:1269–1279. DOI: 10.1007/s00227-006-0282-8.
   Web of Science ®Google Scholar
• Casale P . 2011. Sea turtle by-catch in the Mediterranean. Fish and Fisheries 12:299–316. DOI: 10.1111/j.1467-2979.2010.00394.x.
   Web of Science ®Google Scholar
• Casale P , Freggi D , Basso R , Argano R . 2005. Size at male maturity, sexing methods and adult sex ratio in loggerhead turtles (Caretta caretta) from Italian waters investigated through tail measurements. Journal of Herpetology 15:145–148.
   Google Scholar
• Casale P , Freggi D , Basso R , Vallini C , Argano R . 2007. A model of area fidelity, nomadism, and distribution patterns of loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea. Marine Biology 152:1039–1049. DOI: 10.1007/s00227-007-0752-7.
   Web of Science ®Google Scholar
• Casale P , Freggi D , Cinà A , Rocco M . 2013. Spatio-temporal distribution and migration of adult male loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea: Further evidence of the importance of neritic habitats off North Africa. Marine Biology 160:703–718. DOI: 10.1007/s00227-012-2125-0.
   Web of Science ®Google Scholar
• Casale P , Freggi D , Furii G , Vallini C , Salvemini P , DeFlorio M , Totaro G , Raimondi S , Fortuna C , Godley B . 2015. Annual survival probabilities of juvenile loggerhead sea turtles indicate high anthropogenic impact on Mediterranean populations. Aquatic Conservation: Marine and Freshwater Ecosystems 25:690–700. DOI: 10.1002/aqc.2467.
   Web of Science ®Google Scholar
• Casale P , Laurent L , Gerosa G , Argano R . 2002. Molecular evidence of male-biased dispersal in loggerhead turtle juveniles. Journal of Experimental Marine Biology and Ecology 267:139–145. DOI: 10.1016/S0022-0981(01)00365-3.
   Web of Science ®Google Scholar
• Casale P , Margaritoulis D . 2010. Sea turtles in the Mediterranean: distribution, threats and conservation priorities. Gland, Switzerland: IUCN/SSC Marine Turtle Specialist Group.
   Google Scholar
• Casale P , Simone G . 2017. Seasonal residency of loggerhead turtles Caretta caretta tracked from the Gulf of Manfredonia, South Adriatic. Mediterranean Marine Science 18:4–10. DOI: 10.12681/mms.1663.
   Web of Science ®Google Scholar
• Casale P , Simone G , Conoscitore C , Conoscitore M , Salvemini P . 2012. The Gulf of Manfredonia: A new neritic foraging area for loggerhead sea turtles in the Adriatic Sea. Acta Herpetologica 7:1–12.
   Web of Science ®Google Scholar
• Claudet J , Fraschetti S . 2010. Human-driven impacts on marine habitats: A regional meta-analysis in the Mediterranean Sea. Biological Conservation 143:2195–2206. DOI: 10.1016/j.biocon.2010.06.004.
   Web of Science ®Google Scholar
• Clusa M , Carreras C , Pascual M , Demetropoulos A , Margaritoulis D , Rees AF , Hamza AA , Khalil M , Aureggi M , Levy Y , Türkozan O , Marco A , Aguilar A , Cardona L . 2013. Mitochondrial DNA reveals Pleistocenic colonisation of the Mediterranean by loggerhead turtles (Caretta caretta). Journal of Experimental Marine Biology and Ecology 439:15–24. DOI: 10.1016/j.jembe.2012.10.011.
   Web of Science ®Google Scholar
• Clusa M , Carreras C , Pascual M , Gaughran SJ , Piovano S , Giacoma C , Fernández G , Levy Y , Tomás J , Raga JA , Maffucci F , Hochscheid S , Aguilar A , Cardona L . 2014. Fine-scale distribution of juvenile Atlantic and Mediterranean loggerhead turtles (Caretta caretta) in the Mediterranean Sea. Marine Biology 161:509–519. DOI: 10.1007/s00227-013-2353-y.
   Web of Science ®Google Scholar
• Coll M , Piroddi C , Albouy C , Ben Rais Lasram F , Cheung WWL , Christensen V , Karpouzi VS , Guilhaumon F , Mouillot D , Paleczny M , Palomares ML , Steenbeek J , Trujillo P , Watson R , Pauly D . 2012. The Mediterranean Sea under siege: Spatial overlap between marine biodiversity, cumulative threats and marine reserves. Global Ecology and Biogeography 21:465–480. DOI: 10.1111/j.1466-8238.2011.00697.x.
   Web of Science ®Google Scholar
• Coll M , Piroddi C , Steenbeek J , Kaschner K , Ben Rais Lasram F , Aguzzi J , Ballesteros E , Bianchi CN , Corbera J , Dailianis T , Danovaro R , Estrada M , Froglia C , Galil BS , Gasol JM , Gertwagen R , Gil J , Guilhaumon F , Kesner-Reyes K , Kitsos MS , Koukouras A , Lampadariou N , Laxamana E , de la Cuadra CMLF , Lotze HK , Martin D , Mouillot D , Oro D , Raicevich S , Rius-Barile J , Saiz-Salinas JI , San Vicente C , Somot S , Templado J , Turon X , Vafidis D , Villanueva R , Voultsiadou E . 2010. The biodiversity of the Mediterranean Sea: Estimates, patterns and threats. PLoS ONE 5:e11842.
   PubMed Web of Science ®Google Scholar
• Cuttelod A , Garcia N , Malak DA , Temple H , Katariya V . 2008. The Mediterranean: A biodiversity hotspot under threat. In: Hilton-Taylor and Stuart SN, editors. The 2008 Review of the IUCN Red List of Threatened Species. Gland, Switzerland.
   Google Scholar
• Encalada S , Bjorndal K , Bolten A , Zurita JC , Schroeder B , Possardt E , Sears CJ , Bowen BW . 1998. Population structure of loggerhead turtle (Caretta caretta) nesting colonies in the Atlantic and Mediterranean as inferred from mitochondrial DNA control region sequences. Marine Biology 130:567–575. DOI: 10.1007/s002270050278.
   Web of Science ®Google Scholar
• Garofalo L , Marzano G , Caputo A , Carlino P , Olivieri V , Lorenzini R 2016. Locations of summer meetings…for sea turtles too! Mitochondrial characterization of Caretta caretta nests from the beaches of the southern-middle Adriatic and the northern Ionian Seas. Book of abstracts XI Congresso Nazionale della Societas Herpetologica Italica, 22–25 Settembre 2016, Trento. pp. 131–132.
   Google Scholar
• Garofalo L , Mastrogiacomo A , Casale P , Carlini R , Eleni C , Freggi D , Gelli D , Knittweis L , Mifsud C , Mingozzi T , Novarini N , Scaravelli D , Scillitani G , Oliverio M , Novelletto A . 2013. Genetic characterization of central Mediterranean stocks of the loggerhead turtle (Caretta caretta) using mitochondrial and nuclear markers, and conservation implications. Aquatic Conservation: Marine and Freshwater Ecosystems 23:868–884. DOI: 10.1002/aqc.v23.6.
   Web of Science ®Google Scholar
• Gelman A , Carlin J , Stern HS , Rubin DB . 1996. Bayesian data analysis. New York, NY: Chapman and Hall.
   Google Scholar
• Giovannotti M , Franzellitti S , Nisi Cerioni P , Fabbri E , Guccione S , Vallini C , Tinti F , Caputo V . 2010. Genetic characterization of loggerhead turtle (Caretta caretta) individuals stranded and caught as bycatch from the North-Central Adriatic Sea. Amphibia-Reptilia 31:127–133. DOI: 10.1163/156853810790457902.
   Web of Science ®Google Scholar
• Girard C , Tucker AD , Calmettes B . 2009. Post-nesting migrations of loggerhead sea turtles in the Gulf of Mexico: Dispersal in highly dynamic conditions. Marine Biology 156:1827–1839. DOI: 10.1007/s00227-009-1216-z.
   Web of Science ®Google Scholar
• Grant WS , Milner GB , Krasnowski P , Utter FM . 1980. Use of biochemical genetic variants for identification of sockeye salmon (Oncorhynchus nerka) stocks in Cook Inlet, Alaska. Canadian Journal of Fisheries and Aquatic Sciences 37:1236–1247. DOI: 10.1139/f80-159.
   Web of Science ®Google Scholar
• Hatase H , Kinoshita M , Bando T , Kamezaki N , Sato K , Matsuzawa Y , Goto K , Omuta K , Nakashima Y , Takeshita H , Sakamoto W . 2002. Population structure of loggerhead turtles, Caretta caretta, nesting in Japan: Bottlenecks on the Pacific population. Marine Biology 141:299–305. DOI: 10.1007/s00227-002-0819-4.
   Web of Science ®Google Scholar
• Jensen MP , FitzSimmons NN , Dutton PH . 2013. Molecular genetics of sea turtles. In: Wyneken J , Lohmann KJ , Musick JA , editors. The biology of sea turtles, Volume 3. Boca Raton: CRC Press. pp. 135–154.
   Google Scholar
• Karaa S , Maffucci F , Jribi I , Bologna MA , Borra M , Biffali E , Bradai MN , Hochscheid S . 2016. Connectivity and stock composition of loggerhead turtles foraging on the North African continental shelf (Central Mediterranean): Implications for conservation and management. Marine Ecology 37:1103–1115. DOI: 10.1111/maec.2016.37.issue-5.
   Web of Science ®Google Scholar
• Kumar S , Stecher G , Tamura K . 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870–1874. DOI: 10.1093/molbev/msw054.
   PubMed Web of Science ®Google Scholar
• Laurent L , Casale P , Bradai MN , Godley BJ , Broderick AC , Schroth W , Schierwater B , Levy AM , Freggi D , Abd El-Mawla EM , Hadoud DA , Gomati HE , Domingo M , Hadliehristophorou M , Kornaraky L , Demirayak F , Gautier CH . 1998. Molecular resolution of marine turtle stock composition in fishery bycatch: A case study in the Mediterranean. Molecular Ecology 7:1529–1542. DOI: 10.1046/j.1365-294x.1998.00471.x.
   PubMed Web of Science ®Google Scholar
• Lewison RL , Crowder LB , Read AJ , Freeman SA . 2004. Understanding impacts of fisheries bycatch on marine megafauna. Trends in Ecology & Evolution 19:598–604. DOI: 10.1016/j.tree.2004.09.004.
   Web of Science ®Google Scholar
• Lewison RL , Crowder LB , Wallace BP , Moore JE , Cox T , Zydelis R , McDonald S , DiMatteo A , Dunn DC , Kott CY , Bjorkland R , Kelez S , Soykan C , Stewart KR , Sims M , Boustany A , Read AJ , Halpin P , Nichols WJ , Safina C 2014. Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots. Proceedings of the National Academy of Sciences 111:5271–5276.
   Google Scholar
• Lucchetti A , Pulcinella J , Angelini V , Pari S , Russo T , Cataudella S . 2016. An interaction index to predict turtle bycatch in a Mediterranean bottom trawl fishery. Ecological Indicators 60:557–564. DOI: 10.1016/j.ecolind.2015.07.007.
   Web of Science ®Google Scholar
• Luschi P , Casale P . 2014. Movement patterns of marine turtles in the Mediterranean Sea: A review. Italian Journal of Zoology 81:478–495. DOI: 10.1080/11250003.2014.963714.
   Web of Science ®Google Scholar
• Marcovaldi MÂ , Lopez GG , Soares LS , Lima EHSM , Thom JCA , Almeida AP . 2010. Satellite-tracking of female loggerhead turtles highlights fidelity behavior in northeastern Brazil. Endangered Species Research 12:263–272. DOI: 10.3354/esr00308.
   Google Scholar
• Margaritoulis D , Argano R , Baran I , Bentivegna F , Bradai MN , Camiñas JA , Casale P , De Metrio G , Demetropoulos A , Gerosa G , Godley BJ , Haddoud DA , Houghton J , Laurent L , Lazar B . 2003. Loggerhead turtles in the Mediterranean Sea: Present knowledge and conservation perspectives. In: Bolten AB , Witherington BE , editors. Loggerhead sea turtle. Washington: Smithsonian Books. pp. 175–198.
   Google Scholar
• Margush T , McMorris FR . 1981. Consensus n-trees. Bullettin of Mathematical Biology 43:239–244.
   Web of Science ®Google Scholar
• Marra M , Scillitani G , Flore G , Zaccaria G , Capodiferro T , Ciccolella A , Marzano G , De Franco F , Corriero G . 2015. Analisi cartografica preliminare delle nidificazioni (2006-2013) e realizzazione di un database degli spiaggiamenti (1994-2013) della Tartaruga comune Caretta caretta lungo le coste pugliesi. Atti X Congresso Nazionale Societas Herpetologica Italica, Genova. pp. 393–398.
   Google Scholar
• Moncada F , Abreu-Grobois FA , Bagley D , Bjorndal KA , Bolten AB , Camiñas JA , Ehrhart L , Muhlia-Melo A , Nodarse G , Schroeder BA , Zurita J , Hawkes LA . 2010. Movement patterns of loggerhead turtles Caretta caretta in Cuban waters inferred from flipper tag recaptures. Endangered Species Research 11:61–68. DOI: 10.3354/esr00248.
   Google Scholar
• Myers N , Mittermeier RA , Mittermeier CG , Da Fonseca GAB , Kent J . 2000. Biodiversity hotspots for conservation priorities. Nature 403:853–858. DOI: 10.1038/35002501.
   PubMed Web of Science ®Google Scholar
• Pikesley SK , Broderick AC , Cejudo D , Coyne MS , Godfrey MH , Godley BJ , Lopez P , López-Jurado LF , Merino SE , Varo-Cruz N , Witt MJ , Hawkes LA . 2015. Modelling the niche for a marine vertebrate: A case study incorporating behavioural plasticity, proximate threats and climate change. Ecography 38:803–812. DOI: 10.1111/ecog.2015.v38.i8.
   Web of Science ®Google Scholar
• Rees AF , Carreras C , Broderick AC , Margaritoulis D , Stringell TB , Godley BJ . 2017. Linking loggerhead locations: Using multiple methods to determine the origin of sea turtles in feeding grounds. Marine Biology 164:30. DOI: 10.1007/s00227-016-3055-z.
   Web of Science ®Google Scholar
• Revelles M , Camiñas JA , Cardona L , Parga M , Tomás J , Aguilar A , Alegre F , Raga A , Bertolero A , Oliver G . 2008. Tagging reveals limited exchange of immature loggerhead sea turtles (Caretta caretta) between regions in the western Mediterranean. Scientia Marina 72:511–518.
   Web of Science ®Google Scholar
• Seutin G , White BN , Boag PT . 1991. Preservation of avian blood and tissue samples for DNA analyses. Canadian Journal of Zoology 69:82–90. DOI: 10.1139/z91-013.
   Web of Science ®Google Scholar
• Shamblin BM , Bolten AB , Abreu-Grobois FA , Bjorndal KA , Cardona L , Carreras C , Clusa M , Monzón-Argüello C , Nairn CJ , Nielsen JT , Nel R , Soares LS , Stewart KR , Vilaça ST , Türkozan O , Yilmaz C , Dutton PH . 2014. Geographic patterns of genetic variation in a broadly distributed marine vertebrate: New insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences. PLoS One 9:e85956. DOI: 10.1371/journal.pone.0085956.
   Web of Science ®Google Scholar
• Shamblin BM , Bolten AB , Bjorndal KA , Dutton PH , Nielsen JT , Abreu-Grobois FA , Reich KJ , Witherington BE , Bagley DA , Ehrhart LM . 2012. Expanded mitochondrial control region sequences increase resolution of stock structure among North Atlantic loggerhead turtle rookeries. Marine Ecology Progress Series 469:145–160. DOI: 10.3354/meps09980.
   Web of Science ®Google Scholar
• Stothard P . 2000. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28:1102–1104.
   PubMed Web of Science ®Google Scholar
• Taggart JB , Hynes RA , Prodouhl PA , Ferguson A . 1992. A simplified protocol for routine total DNA isolation from salmonid fishes. Journal of Fish Biology 40:963–965. DOI: 10.1111/jfb.1992.40.issue-6.
   Web of Science ®Google Scholar
• Thompson JD , Higgins DG , Gibson TJ . 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22:4673–4680. DOI: 10.1093/nar/22.22.4673.
   PubMed Web of Science ®Google Scholar
• Wallace BP , DiMatteo AD , Bolten AB , Chaloupka MY , Hutchinson BJ , Abreu-Grobois A , Mortimer JA , Seminoff JA , Amorocho D , Bjorndal KA , Bourjea J , Bowen BW , Dueñas RB , Casale P , Choudhury BC , Costa A , Dutton PH , Fallabrino A , Finkbeiner EM , Girard A , Girondot M , Hamann M , Hurley BJ , López-Mendilaharsu M , Marcovaldi MA , Musick JA , Nel R , PIlcher NJ , Troëng S , Witherington B , Mast RB . 2011. Global conservation priorities for marine turtles. PLoS ONE 6:e24510. DOI: 10.1371/journal.pone.0024510.
   PubMed Web of Science ®Google Scholar
• Witt MJ , Hawkes LA , Godfrey MH , Godley BJ , Broderick AC . 2010. Predicting the impacts of climate change on a globally distributed species: The case of the loggerhead turtle. Journal of Experimental Biology 213:901–911. DOI: 10.1242/jeb.038133.
   PubMed Web of Science ®Google Scholar
• Yilmaz C , Turkozan O , Bardakci F , White M , Kararaj E . 2012. Loggerhead turtles (Caretta caretta) foraging at Drini Bay in Northern Albania: Genetic characterization reveals new haplotypes. Acta Herpetologica 7:155–162.
   Web of Science ®Google Scholar